This situation is a bit deeper than anyone can know from an external perspective. If you have a system administrator that you trust, you should ask them to review that server for you. Files don’t really just go missing from a reboot, and it’s especially odd if they do and yet the operating system still boots (as that kind of file system corruption is unlikely to specifically target items non-essential to boot).

My concern is that your server was compromised and configured by an attacker to act this way. Most likely you’re not going to restore that data in a meaningful way and should start pulling your external backups. I would not re-deploy on this server, but I would have a sysadmin look at it to see if any evidence remains of what occurred so that it might be prevented.